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Analyzing Trace-Level Impurities of a Pharmaceutical Intermediate Using ,,, an LCQ Deca Ion Trap Mass Spectrometer and the Mass Frontier ,,, Software Package

imental MS2 spectrum then it should have m/z values of M+2, M+52, and M+70 in the experimental MS2 spectra of the dihydro, hydroxychloro, and dichloro substituted impurities, respectively).

In Table 1, fragment ions that have been assigned the same mechanism of formation by Mass Frontier are highlighted with the same color. Taking this into account the table reveals that in all cases, fragment ions related by a common Mass Frontier predicted mechanism of formation either have the same experimental m/z value or have experimental m/z values that differ by the mass of the substituents depending on whether or not the fragment structure resulting from the Mass Frontier prediction contains the proposed site of substitution. This observation provides the main verification for the impurity structures that were proposed.



Conclusions

With the help of Data Dependent MS2 scanning with Dynamic Exclusion, three impurities of a proprietary pharmaceutical intermediate were detected at or below the 0.1% level and targeted for characterization. Isotopic patterns and mass differences provided the rationale for proposed structures that were
submitted to Mass Frontier for verification.

The structures proposed for the impurities were confirmed by a comparison of Mass Frontiers fragmentation predictions with the experimental MS2 spectra. The analysis supported the conclusion that all three of the impurities resulted from chemical substitutions on a specific double bond in the intermediate.

The characterization of impurities present in amounts as low as 0.1% of the parent abundance is
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